# 单细胞 RNA-seq

涵盖完整单细胞工作流的教程：比对、预处理、注释、轨迹分析、细胞结构分析、速度分析和多组学。

## 比对

```{toctree}
:maxdepth: 1

../Tutorials-single/t_alignment_1k
../Tutorials-single/t_alignment_velocity
```

## 预处理

```{toctree}
:maxdepth: 1

../Tutorials-single/t_preprocess_cpu
../Tutorials-single/t_preprocess_gpu
../Tutorials-single/t_cluster
../Tutorials-single/t_single_batch
../Tutorials-single/t_cnmf
../Tutorials-single/t_lazy
```

## 注释

```{toctree}
:maxdepth: 2

../Tutorials-single/t_anno_noref
../Tutorials-single/t_anno_ref
../Tutorials-single/t_cellvote
../Tutorials-single/t_cellmatch
../Tutorials-single/anno-zoo/index
```

## 轨迹

```{toctree}
:maxdepth: 1

../Tutorials-single/t_cytotrace
../Tutorials-single/t_traj_diffusion
../Tutorials-single/t_traj_slingshot
../Tutorials-single/t_traj_palantir
../Tutorials-single/t_traj_sctour
../Tutorials-single/t_traj_monocle2
../Tutorials-single/t_traj_stavia
../Tutorials-single/t_traj_stavia_toy_multifurcating
../Tutorials-single/t_via
../Tutorials-single/t_via_velo
../Tutorials-single/t_cellfate_gene
../Tutorials-single/t_cellfate
```

## 细胞结构

```{toctree}
:maxdepth: 1

../Tutorials-single/t_metacells
../Tutorials-single/t_deg_single
../Tutorials-single/t_scdeg
../Tutorials-single/t_scenic
../Tutorials-single/t_scdrug
../Tutorials-single/t_simba
```

## 拷贝数变异

```{toctree}
:maxdepth: 1

../Tutorials-single/t_copykat
../Tutorials-single/t_infercnv
```

## 富集分析

```{toctree}
:maxdepth: 1

../Tutorials-single/t_aucell
../Tutorials-single/enrichment/t_es_compare
```

## 细胞-细胞通讯

```{toctree}
:maxdepth: 1

../Tutorials-single/t_ccc_cellphonedb
../Tutorials-single/t_ccc_liana
```

## 速度分析

```{toctree}
:maxdepth: 1

../Tutorials-velo/t_velo
../Tutorials-velo/t_graphvelo
../Tutorials-velo/t_regvelo
../Tutorials-velo/t_regvelo_infer_grn
../Tutorials-velo/t_velo_cellrank
```

## 多组学

```{toctree}
:maxdepth: 1

../Tutorials-single/t_mofa
../Tutorials-single/t_mofa_glue
../Tutorials-single/t_anno_trans
```